principal coordinate analysis
I want to compare 2 groups of 60 members with 1600 samples for which I have sequence counts. There are lots of zeros and maxima in the millions. For data visualisation, do I have to prepare my dataset? For heatmaps I square root transformed the set (parts of it). Would anyone know how to go about it in PCoA or have a link to read up on it?
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rene.j.erhardt •
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You should go with normalized counts, and maybe you can remove the lower 10% of variables based on variance. You may have a look at PCAtools : https://bioconductor.org/packages/devel/bioc/vignettes/PCAtools/inst/doc/PCAtools.html